OAT

ornithine aminotransferase

Basic information

Region (hg38): 10:124397303-124418976

Links

ENSG00000065154 ∙ NCBI:4942 ∙ OMIM:613349 ∙ HGNC:8091 ∙ Uniprot:P04181 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ornithine aminotransferase deficiency (Supportive), mode of inheritance: AR
• ornithine aminotransferase deficiency (Strong), mode of inheritance: AR
• ornithine aminotransferase deficiency (Definitive), mode of inheritance: AR
• ornithine aminotransferase deficiency (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Gyrate atrophy of choroid and retina	AR	Biochemical	Dietary management (eg, with arginine restriction) may be beneficial	Biochemical; Musculoskeletal; Neurologic; Ophthalmologic	4122112; 572946; 7444439; 7356686; 3339136; 1737786; 11831916; 10604138; 110617919; 1297489; 15750329; 22674428; 34340878

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OAT gene.

• Ornithine_aminotransferase_deficiency (617 variants)
• Inborn_genetic_diseases (61 variants)
• not_provided (34 variants)
• Hyperornithinemia (14 variants)
• Retinal_dystrophy (11 variants)
• not_specified (9 variants)
• OAT-related_disorder (8 variants)
• Gyrate_atrophy_of_choroid_and_retina_with_pyridoxine-responsive_ornithinemia (2 variants)
• Pain (1 variants)
• Visual_field_defect (1 variants)
• Abnormal_choroid_morphology (1 variants)
• Optic_atrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OAT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000274.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		1	5	182		188
missense	10	35	178	8	1	232
nonsense	15	16	1			32
start loss	3					3
frameshift	21	30				51
splice donor/acceptor (+/-2bp)	6	21	2			29
Total	55	103	186	190	1

Highest pathogenic variant AF is 0.000119590986

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OAT	protein_coding	protein_coding	ENST00000368845	9	21674

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.876	204	242	0.842	0.0000129	2848
Missense in Polyphen		63	92.108	0.68398		1129
Synonymous	1.01	81	93.4	0.867	0.00000563	882
Loss of Function	1.70	13	21.5	0.605	0.00000121	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000359	0.000358
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000246	0.000246
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Hyperornithinemia with gyrate atrophy of choroid and retina (HOGA) [MIM:258870]: A disorder clinically characterized by a triad of progressive chorioretinal degeneration, early cataract formation, and type II muscle fiber atrophy. Characteristic chorioretinal atrophy with progressive constriction of the visual fields leads to blindness at the latest during the sixth decade of life. Patients generally have normal intelligence. {ECO:0000269|PubMed:1612597, ECO:0000269|PubMed:1737786, ECO:0000269|PubMed:23076989, ECO:0000269|PubMed:2793865, ECO:0000269|PubMed:3375240, ECO:0000269|PubMed:7668253, ECO:0000269|PubMed:7887415}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);Hyperornithinemia with gyrate atrophy (HOGA);Creatine deficiency, guanidinoacetate methyltransferase deficiency;L-arginine:glycine amidinotransferase deficiency;Hyperornithinemia-hyperammonemia-homocitrullinuria [HHH-syndrome];Guanidinoacetate Methyltransferase Deficiency (GAMT Deficiency);Prolinemia Type II;Prolidase Deficiency (PD);Arginine and Proline Metabolism;Hyperprolinemia Type I;Hyperprolinemia Type II;Ornithine Aminotransferase Deficiency (OAT Deficiency);Arginine: Glycine Amidinotransferase Deficiency (AGAT Deficiency);Amino Acid metabolism;Urea cycle and metabolism of amino groups;Metabolism of amino acids and derivatives;Metabolism;ornithine <i>de novo </i> biosynthesis;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Arginine Proline metabolism;Amino acid synthesis and interconversion (transamination) (Consensus)

Recessive Scores

• pRec: 0.642

Intolerance Scores

• loftool: 0.0996
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.33

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: visual perception;cellular amino acid biosynthetic process;arginine catabolic process to proline via ornithine;arginine catabolic process to glutamate;protein hexamerization;L-proline biosynthetic process
• Cellular component: nucleoplasm;cytoplasm;mitochondrion;mitochondrial matrix
• Molecular function: ornithine-oxo-acid transaminase activity;pyridoxal phosphate binding